In my best friend's family, all the males' first name starts with a W and second name with a J, as decreed by his grandfather. So him, his uncles, and cousins, all have the initials W J [Surname], irrespective of whether you carry the family name.
If the OP's wife was was related to him by blood before their marriage (very common on the far east rand) I see no problem with their son having the same names as the dad. Cut him some slack people.